Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005535.1 Hibiscus syriacus cultivar Beakdansim tig00012803_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 66570
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:2834 original size:34 final size:34
Alignment explanation
Indices: 2794--2953 Score: 170
Period size: 33 Copynumber: 4.7 Consensus size: 34
2784 GAAGGTTTGG
*
2794 TGTTTCAAGAGAAATGTTTTCAAAGGTTTTTTTT
1 TGTTTCAAGAGAAATGATTTCAAAGGTTTTTTTT
**
2828 TGTTTCAAGAGAAACAATTTCAAAGGGTTTTTTTTT
1 TGTTTCAAGAGAAATGATTTCAAA-GG-TTTTTTTT
*
2864 GTGTTTCAAGAGAAACTG-TCTT--AAGGATTTTTTT
1 -TGTTTCAAGAGAAA-TGAT-TTCAAAGGTTTTTTTT
*
2898 TGTTTCAAGA-AAACTG-TTTCAAAGGTTTTTTTG
1 TGTTTCAAGAGAAA-TGATTTCAAAGGTTTTTTTT
*
2931 TGTTTC-AGAGAAATAATTTCAAA
1 TGTTTCAAGAGAAATGATTTCAAA
2954 TATTGGTGCT
Statistics
Matches: 108, Mismatches: 9, Indels: 19
0.79 0.07 0.14
Matches are distributed among these distances:
31 2 0.02
32 11 0.10
33 36 0.33
34 28 0.26
35 4 0.04
36 10 0.09
37 15 0.14
38 2 0.02
ACGTcount: A:0.30, C:0.08, G:0.17, T:0.44
Consensus pattern (34 bp):
TGTTTCAAGAGAAATGATTTCAAAGGTTTTTTTT
Found at i:2902 original size:33 final size:35
Alignment explanation
Indices: 2793--2943 Score: 158
Period size: 34 Copynumber: 4.4 Consensus size: 35
2783 CGAAGGTTTG
*
2793 GTGTTTCAAGAGAAA-TGTTTTCAAAGGTTTTTTTT
1 GTGTTTCAAGAGAAACTGTCTT-AAAGGTTTTTTTT
**
2828 -TGTTTCAAGAGAAACAAT-TTCAAAGGGTTTTTTTTT
1 GTGTTTCAAGAGAAACTGTCTT-AAA-GG-TTTTTTTT
*
2864 GTGTTTCAAGAGAAACTGTCTT-AAGGATTTTTTT
1 GTGTTTCAAGAGAAACTGTCTTAAAGGTTTTTTTT
2898 -TGTTTCAAGA-AAACTGT-TTCAAAGG-TTTTTTT
1 GTGTTTCAAGAGAAACTGTCTT-AAAGGTTTTTTTT
2930 GTGTTTC-AGAGAAA
1 GTGTTTCAAGAGAAA
2944 TAATTTCAAA
Statistics
Matches: 102, Mismatches: 5, Indels: 20
0.80 0.04 0.16
Matches are distributed among these distances:
31 2 0.02
32 17 0.17
33 23 0.23
34 27 0.26
35 5 0.05
36 10 0.10
37 16 0.16
38 2 0.02
ACGTcount: A:0.28, C:0.08, G:0.19, T:0.44
Consensus pattern (35 bp):
GTGTTTCAAGAGAAACTGTCTTAAAGGTTTTTTTT
Found at i:3017 original size:36 final size:36
Alignment explanation
Indices: 2963--3344 Score: 333
Period size: 36 Copynumber: 11.1 Consensus size: 36
2953 ATATTGGTGC
2963 TTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTGT
* * * *
3000 TCCAA-AGAAACTATCTCAAGGGAGACGAAATTTGT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGT
* *
3035 TTCAAG-GAAAACAGAT-TC-A-A-AG----ATTTTGT
1 TTCAAGAG-AAACTG-TCTCAAGAGAGACAAAATTTGT
*
3064 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGT
*
3100 TTCTA-A-AAA-TGTCTCAAGAGAGACAAAATTTGT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGT
* *
3133 TTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTGT
* * * *
3170 TCCAAAAG-AACTGTCTCAAGGGAGACGAAATTTGT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGT
** *
3205 TTCAAG-GAAAACAAAT-TC-A-A-AG----ATTTTGT
1 TTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAATTTGT
*
3234 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGT
* *
3270 TTTAAGAGAAAATGTCTCAAGAGAGACAAAATTTGT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGT
* * *
3306 TTTAAGAGAAACTGTATTAAGAGAGACAAAACTTTGT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTGT
3343 TT
1 TT
3345 TGAGTAAATT
Statistics
Matches: 279, Mismatches: 37, Indels: 58
0.75 0.10 0.16
Matches are distributed among these distances:
28 2 0.01
29 37 0.13
30 4 0.01
31 2 0.01
32 4 0.01
33 31 0.11
34 5 0.02
35 23 0.08
36 149 0.53
37 22 0.08
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (36 bp):
TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGT
Found at i:3075 original size:101 final size:99
Alignment explanation
Indices: 2963--3143 Score: 265
Period size: 101 Copynumber: 1.8 Consensus size: 99
2953 ATATTGGTGC
* *
2963 TTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTCCAAAGAAACTATCTCAAGGGAGACGA
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTGTTCCAAA-AAA-TATCTCAAGAGAGACAA
3028 AATTTGTTTCAAG-GAAAACAGATTCAAAGATTTTGT
63 AATTTGTTTCAAGAGAAAACAGATTCAAAGATTTTGT
* * * *
3064 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCTAAAAATGTCTCAAGAGAGACAAAAT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTCCAAAAAATATCTCAAGAGAGACAAAAT
*
3129 TTGTTTTAAGAGAAA
66 TTGTTTCAAGAGAAA
3144 CTGTCTCAAG
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
98 26 0.36
99 7 0.10
100 9 0.12
101 30 0.42
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (99 bp):
TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTCCAAAAAATATCTCAAGAGAGACAAAAT
TTGTTTCAAGAGAAAACAGATTCAAAGATTTTGT
Found at i:3153 original size:170 final size:171
Alignment explanation
Indices: 2966--3343 Score: 654
Period size: 170 Copynumber: 2.2 Consensus size: 171
2956 TTGGTGCTTC
2966 AAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTCC-AAAGAAACTATCTCAAGGGAGACGAAA
1 AAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTCCAAAAG-AACTATCTCAAGGGAGACGAAA
*
3030 TTTGTTTCAAGGAAAACAGATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
65 TTTGTTTCAAGGAAAACAAATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
3095 TTTGTTTCT-A-AAAATGTCTCAAGAGAGACAAAATTTGTTTT
130 TTTGTTT-TAAGAAAATGTCTCAAGAGAGACAAAATTTGTTTT
* *
3136 AAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAACTGTCTCAAGGGAGACGAAAT
1 AAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTCCAAAAGAACTATCTCAAGGGAGACGAAAT
3201 TTGTTTCAAGGAAAACAAATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAT
66 TTGTTTCAAGGAAAACAAATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAT
3266 TTGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAATTTGTTTT
131 TTGTTTT-A-AGAAAATGTCTCAAGAGAGACAAAATTTGTTTT
* *
3309 AAGAGAAACTGTATTAAGAGAGACAAAACTTTGTT
1 AAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTT
3344 TTGAGTAAAT
Statistics
Matches: 197, Mismatches: 6, Indels: 7
0.94 0.03 0.03
Matches are distributed among these distances:
169 1 0.01
170 128 0.65
171 4 0.02
172 1 0.01
173 63 0.32
ACGTcount: A:0.42, C:0.13, G:0.19, T:0.26
Consensus pattern (171 bp):
AAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTCCAAAAGAACTATCTCAAGGGAGACGAAAT
TTGTTTCAAGGAAAACAAATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAT
TTGTTTTAAGAAAATGTCTCAAGAGAGACAAAATTTGTTTT
Found at i:3261 original size:101 final size:102
Alignment explanation
Indices: 3128--3316 Score: 265
Period size: 101 Copynumber: 1.9 Consensus size: 102
3118 AGAGACAAAA
* * *
3128 TTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAG-AACTGTCTCAAGGG
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTAGTTCCAAAAGAAAATGTCTCAAGAG
*
3192 AGACGAAATTTGTTTCAAG-GAAAACAAATTCAAAGAT
65 AGACAAAATTTGTTTCAAGAGAAAACAAATTCAAAGAT
* * ** *
3229 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAAATGTCTCAAGAGA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAAAGAAAATGTCTCAAGAGA
*
3294 GACAAAATTTGTTTTAAGAGAAA
66 GACAAAATTTGTTTCAAGAGAAA
3317 CTGTATTAAG
Statistics
Matches: 76, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
100 9 0.12
101 63 0.83
102 4 0.05
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.28
Consensus pattern (102 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAAAGAAAATGTCTCAAGAGA
GACAAAATTTGTTTCAAGAGAAAACAAATTCAAAGAT
Found at i:3313 original size:19 final size:19
Alignment explanation
Indices: 3255--3314 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
3245 CTGTCTCAAG
3255 AGAGACAAAATTTGTTTTA
1 AGAGACAAAATTTGTTTTA
**
3274 AGAG--AAAA--TGTCTCAA
1 AGAGACAAAATTTGT-TTTA
3290 GAGAGACAAAATTTGTTTTA
1 -AGAGACAAAATTTGTTTTA
3310 AGAGA
1 AGAGA
3315 AACTGTATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 12
0.66 0.09 0.26
Matches are distributed among these distances:
15 3 0.10
16 2 0.06
17 8 0.26
19 13 0.42
20 2 0.06
21 3 0.10
ACGTcount: A:0.45, C:0.07, G:0.20, T:0.28
Consensus pattern (19 bp):
AGAGACAAAATTTGTTTTA
Found at i:9108 original size:3 final size:3
Alignment explanation
Indices: 9100--9196 Score: 133
Period size: 3 Copynumber: 32.3 Consensus size: 3
9090 AAACAAAACC
9100 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * *
9148 ATA ATA GTA ATA GTA ATA ATA TATA CTA ATA TTA ATA TTA ATA A-A
1 ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
9193 ATA A
1 ATA A
9197 ATAAGAAAAT
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
2 2 0.02
3 77 0.94
4 3 0.04
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:9332 original size:16 final size:16
Alignment explanation
Indices: 9307--9361 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 16
9297 ACATATAATT
*
9307 AAATATTAGAGGAAA-A
1 AAATAATAGA-GAAATA
9323 AAATAATAGAGAAATA
1 AAATAATAGAGAAATA
* *
9339 TAATAATA-AAAAATA
1 AAATAATAGAGAAATA
*
9354 TAATAATA
1 AAATAATA
9362 ATAAAATGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
15 18 0.51
16 17 0.49
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (16 bp):
AAATAATAGAGAAATA
Found at i:9352 original size:15 final size:15
Alignment explanation
Indices: 9324--9368 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
9314 AGAGGAAAAA
*
9324 AATAATAGAGAAATAT
1 AATAATA-AAAAATAT
9340 AATAATAAAAAATAT
1 AATAATAAAAAATAT
9355 AATAATAATAAAAT
1 AATAATAA-AAAAT
9369 GAAATAGTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 15 0.56
16 12 0.44
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (15 bp):
AATAATAAAAAATAT
Found at i:10619 original size:14 final size:14
Alignment explanation
Indices: 10578--10625 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
10568 AAGTATTTTC
10578 CTTAAATTTTAAAT
1 CTTAAATTTTAAAT
*
10592 -TTCAAGTTTTAAAT
1 CTT-AAATTTTAAAT
*
10606 CTTAAATTTAAAAT
1 CTTAAATTTTAAAT
*
10620 CCTAAA
1 CTTAAA
10626 ACTTAGACAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 2 0.07
14 24 0.86
15 2 0.07
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (14 bp):
CTTAAATTTTAAAT
Found at i:30238 original size:33 final size:33
Alignment explanation
Indices: 30196--30262 Score: 118
Period size: 33 Copynumber: 2.0 Consensus size: 33
30186 AAGGCTGCCA
30196 GTGGAGGAGTCCTCCGAGATACCAACT-GAGAGT
1 GTGGAGGAGTCCTCCGAGATACCAA-TGGAGAGT
30229 GTGGAGGAGTCCTCCGAGATACCAATGGAGAGT
1 GTGGAGGAGTCCTCCGAGATACCAATGGAGAGT
30262 G
1 G
30263 AGTAGCGGGC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 1 0.03
33 32 0.97
ACGTcount: A:0.27, C:0.19, G:0.36, T:0.18
Consensus pattern (33 bp):
GTGGAGGAGTCCTCCGAGATACCAATGGAGAGT
Found at i:31950 original size:39 final size:40
Alignment explanation
Indices: 31893--31984 Score: 107
Period size: 39 Copynumber: 2.3 Consensus size: 40
31883 ATATCTCGGG
* * *
31893 GTCTTCAACATAATTTGCATGCAAA-ATCGAATCTCTAGGC
1 GTCTTTAACACAATTTGCATGCAAACAT-GAAGCTCTAGGC
* * *
31933 GTCTTTAACACAA-TTGCATTCAAACATGGAGGTCTAGGC
1 GTCTTTAACACAATTTGCATGCAAACATGAAGCTCTAGGC
31972 GTCTTTAACACAA
1 GTCTTTAACACAA
31985 AACATGGAGG
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
39 32 0.71
40 13 0.29
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (40 bp):
GTCTTTAACACAATTTGCATGCAAACATGAAGCTCTAGGC
Found at i:31988 original size:30 final size:30
Alignment explanation
Indices: 31954--32014 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
31944 AATTGCATTC
31954 AAACATGGAGGTCTAGGCGTCTTTAACACA
1 AAACATGGAGGTCTAGGCGTCTTTAACACA
31984 AAACATGGAGGTCTAGGCGTCTTTAACACA
1 AAACATGGAGGTCTAGGCGTCTTTAACACA
32014 A
1 A
32015 TTCAAGGAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.23
Consensus pattern (30 bp):
AAACATGGAGGTCTAGGCGTCTTTAACACA
Found at i:32024 original size:30 final size:30
Alignment explanation
Indices: 31954--32036 Score: 112
Period size: 30 Copynumber: 2.8 Consensus size: 30
31944 AATTGCATTC
*
31954 AAACATGGAGGTCTAGGCGTCTTTAACACA
1 AAACAAGGAGGTCTAGGCGTCTTTAACACA
*
31984 AAACATGGAGGTCTAGGCGTCTTTAACACA
1 AAACAAGGAGGTCTAGGCGTCTTTAACACA
** * *
32014 ATTCAAGGAGGTCTCGGTGTCTT
1 AAACAAGGAGGTCTAGGCGTCTT
32037 CAAATTCAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (30 bp):
AAACAAGGAGGTCTAGGCGTCTTTAACACA
Found at i:35446 original size:22 final size:22
Alignment explanation
Indices: 35405--35446 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
35395 AATCTTATTA
*
35405 TTTTATAAATTTTTTAATTAAT
1 TTTTATAAATTTTGTAATTAAT
35427 TTTTAT-AATTTTGTAGATTA
1 TTTTATAAATTTTGTA-ATTA
35447 TATTATATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (22 bp):
TTTTATAAATTTTGTAATTAAT
Found at i:35588 original size:14 final size:14
Alignment explanation
Indices: 35569--35637 Score: 61
Period size: 14 Copynumber: 4.9 Consensus size: 14
35559 TAGTAAAATT
35569 TAATGATTTAATAA
1 TAATGATTTAATAA
*
35583 TAATGATTTAATCAT
1 TAATGATTTAAT-AA
* *
35598 TATTAAATTT--TAA
1 TAAT-GATTTAATAA
*
35611 CTATTGATTTAATAA
1 -TAATGATTTAATAA
35626 TAATGATTTAAT
1 TAATGATTTAAT
35638 GATTTAATAC
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
13 5 0.11
14 28 0.64
15 7 0.16
16 4 0.09
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (14 bp):
TAATGATTTAATAA
Found at i:35639 original size:8 final size:8
Alignment explanation
Indices: 35626--35672 Score: 55
Period size: 8 Copynumber: 6.2 Consensus size: 8
35616 GATTTAATAA
35626 TAATGATT
1 TAATGATT
35634 TAATGATT
1 TAATGATT
*
35642 TAAT-A-C
1 TAATGATT
35648 TAATGATT
1 TAATGATT
*
35656 TGAT-ATT
1 TAATGATT
35663 TAATGATT
1 TAATGATT
35671 TA
1 TA
35673 GTAATGATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
6 4 0.12
7 8 0.25
8 20 0.62
ACGTcount: A:0.38, C:0.02, G:0.11, T:0.49
Consensus pattern (8 bp):
TAATGATT
Found at i:35643 original size:22 final size:22
Alignment explanation
Indices: 35566--35666 Score: 91
Period size: 22 Copynumber: 4.7 Consensus size: 22
35556 TAATAGTAAA
35566 ATTTAATGATTTAATAATAATG
1 ATTTAATGATTTAATAATAATG
* * * *
35588 ATTTAATCA-TTATTAA-ATTTT
1 ATTTAATGATTTAATAATA-ATG
** *
35609 AACTATTGATTTAATAATAATG
1 ATTTAATGATTTAATAATAATG
*
35631 ATTTAATGATTTAATACTAATG
1 ATTTAATGATTTAATAATAATG
*
35653 ATTTGAT-ATTTAAT
1 ATTTAATGATTTAAT
35667 GATTTAGTAA
Statistics
Matches: 60, Mismatches: 16, Indels: 7
0.72 0.19 0.08
Matches are distributed among these distances:
20 1 0.02
21 19 0.32
22 39 0.65
23 1 0.02
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.49
Consensus pattern (22 bp):
ATTTAATGATTTAATAATAATG
Found at i:35651 original size:14 final size:15
Alignment explanation
Indices: 35634--35672 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
35624 AATAATGATT
35634 TAATGATTTAATA-C
1 TAATGATTTAATATC
* *
35648 TAATGATTTGATATT
1 TAATGATTTAATATC
35663 TAATGATTTA
1 TAATGATTTA
35673 GTAATGATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.49
Consensus pattern (15 bp):
TAATGATTTAATATC
Found at i:36464 original size:21 final size:21
Alignment explanation
Indices: 36422--36464 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
36412 TTTCTGGGCT
* *
36422 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
36443 AGGGGAATCGATTCCCCCTCA
1 AGGGGAATCGATACCCACTCA
36464 A
1 A
36465 ACGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:37164 original size:23 final size:23
Alignment explanation
Indices: 37113--37181 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 23
37103 CATTATTATA
* *
37113 TGGCACTACAGTGCAATTCTATG
1 TGGCACTACGGTGCAATTCTACG
** *
37136 CAGCACTCCGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* * *
37159 TGGCACTTCGTTGCAATTATACG
1 TGGCACTACGGTGCAATTCTACG
37182 AGCTGTGGTG
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.29
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:39809 original size:24 final size:21
Alignment explanation
Indices: 39760--39809 Score: 55
Period size: 24 Copynumber: 2.2 Consensus size: 21
39750 GGCTCCGAAA
*
39760 GAATTGCAAGAGTTAAAGAAT
1 GAATTGCAAGAGTTAAAGAAG
*
39781 CAATTGCAAGAGCTGTTAAAGAAG
1 GAATTGCAAGA---GTTAAAGAAG
39805 GAATT
1 GAATT
39810 TATTCGACCA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 10 0.43
24 13 0.57
ACGTcount: A:0.44, C:0.08, G:0.24, T:0.24
Consensus pattern (21 bp):
GAATTGCAAGAGTTAAAGAAG
Found at i:43951 original size:23 final size:23
Alignment explanation
Indices: 43917--44003 Score: 138
Period size: 23 Copynumber: 3.8 Consensus size: 23
43907 CATTATTATA
*
43917 TGGCACTACGGTGCAATTCTACG
1 TGGCACTCCGGTGCAATTCTACG
*
43940 CGGCACTCCGGTGCAATTCTACG
1 TGGCACTCCGGTGCAATTCTACG
43963 TGGCACTCCGGTGCAATTCTACG
1 TGGCACTCCGGTGCAATTCTACG
* *
43986 TGGCACTTCGGTACAATT
1 TGGCACTCCGGTGCAATT
44004 ATATGAGCTG
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 59 1.00
ACGTcount: A:0.20, C:0.29, G:0.25, T:0.26
Consensus pattern (23 bp):
TGGCACTCCGGTGCAATTCTACG
Found at i:44626 original size:14 final size:14
Alignment explanation
Indices: 44604--44670 Score: 91
Period size: 14 Copynumber: 4.8 Consensus size: 14
44594 ATGATACTAA
44604 TAATGATTTAACTT
1 TAATGATTTAACTT
* *
44618 TAATAATTTAA-TAA
1 TAATGATTTAACT-T
*
44632 TAATTATTTAACTT
1 TAATGATTTAACTT
44646 TAATGATTTAACTT
1 TAATGATTTAACTT
44660 TAATGATTTAA
1 TAATGATTTAA
44671 TAATAATAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
13 1 0.02
14 44 0.96
15 1 0.02
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.49
Consensus pattern (14 bp):
TAATGATTTAACTT
Found at i:44635 original size:28 final size:29
Alignment explanation
Indices: 44599--44670 Score: 103
Period size: 28 Copynumber: 2.6 Consensus size: 29
44589 AAATAATGAT
44599 ACTAATAATGATTTAACTTTAATAATTTA
1 ACTAATAATGATTTAACTTTAATAATTTA
* *
44628 A-TAATAATTATTTAACTTTAATGATTTA
1 ACTAATAATGATTTAACTTTAATAATTTA
*
44656 ACT-TTAATGATTTAA
1 ACTAATAATGATTTAA
44671 TAATAATAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 36 0.95
29 2 0.05
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (29 bp):
ACTAATAATGATTTAACTTTAATAATTTA
Found at i:47629 original size:22 final size:23
Alignment explanation
Indices: 47586--47630 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
47576 TTTTTATAAA
47586 CGTCCCGTGCATTGAATTATTGG
1 CGTCCCGTGCATTGAATTATTGG
* *
47609 CGTCTCGTGCA-TGCATTATTGG
1 CGTCCCGTGCATTGAATTATTGG
47631 TGGACCTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.16, C:0.22, G:0.27, T:0.36
Consensus pattern (23 bp):
CGTCCCGTGCATTGAATTATTGG
Found at i:47652 original size:33 final size:33
Alignment explanation
Indices: 47603--47696 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
47593 TGCATTGAAT
*
47603 TATTGGCGTCTCGTGCATGCATTATTGGTGGACC
1 TATT-GCGTCCCGTGCATGCATTATTGGTGGACC
*
47637 TATTGCGTCCTGTGCATGCATTATTGGTGGACC
1 TATTGCGTCCCGTGCATGCATTATTGGTGGACC
47670 TATTGCGTCCCGTGCATGCATTATTGG
1 TATTGCGTCCCGTGCATGCATTATTGG
47697 ATGAAGAAGA
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 53 0.93
34 4 0.07
ACGTcount: A:0.15, C:0.21, G:0.28, T:0.36
Consensus pattern (33 bp):
TATTGCGTCCCGTGCATGCATTATTGGTGGACC
Found at i:52163 original size:30 final size:29
Alignment explanation
Indices: 52129--52190 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 29
52119 ATCTATACTT
**
52129 TTTTAAAAATATATGTTCATCTCATTCAAA
1 TTTTAAAAATATAAATTCATCTC-TTCAAA
* * *
52159 TTTTATAAATTTAAATTCATCTCTTTAAA
1 TTTTAAAAATATAAATTCATCTCTTCAAA
52188 TTT
1 TTT
52191 AAATTCATCC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 8 0.30
30 19 0.70
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50
Consensus pattern (29 bp):
TTTTAAAAATATAAATTCATCTCTTCAAA
Found at i:52205 original size:19 final size:20
Alignment explanation
Indices: 52164--52205 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
52154 TCAAATTTTA
52164 TAAATTTAAATTCATCTCTT
1 TAAATTTAAATTCATCTCTT
52184 TAAATTTAAATTCATC-CTT
1 TAAATTTAAATTCATCTCTT
52203 TAA
1 TAA
52206 CCTAAAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.38, C:0.14, G:0.00, T:0.48
Consensus pattern (20 bp):
TAAATTTAAATTCATCTCTT
Found at i:52213 original size:19 final size:20
Alignment explanation
Indices: 52171--52214 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
52161 TTATAAATTT
* *
52171 AAATTCATCTCTTTAAATTT
1 AAATTCATCTCTTTAAACTA
*
52191 AAATTCATC-CTTTAACCTA
1 AAATTCATCTCTTTAAACTA
52210 AAATT
1 AAATT
52215 TTATACGTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.39, C:0.18, G:0.00, T:0.43
Consensus pattern (20 bp):
AAATTCATCTCTTTAAACTA
Found at i:52477 original size:17 final size:17
Alignment explanation
Indices: 52446--52483 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
52436 TATTTTATTT
52446 TATTATATATATATATA
1 TATTATATATATATATA
52463 TATTA-ATATAGTATATA
1 TATTATATATA-TATATA
52480 TATT
1 TATT
52484 TTTTTAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TATTATATATATATATA
Found at i:52554 original size:26 final size:26
Alignment explanation
Indices: 52497--52559 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
52487 TTAGAAAATG
** * *
52497 GTTTTTGAAAATTTATATATTATATA
1 GTTTTTGAAAACATATATAATATACA
*
52523 GGTTTTGAAAACATATATAATATACA
1 GTTTTTGAAAACATATATAATATACA
*
52549 GTTTTTAAAAA
1 GTTTTTGAAAA
52560 AAATTCTGAA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (26 bp):
GTTTTTGAAAACATATATAATATACA
Found at i:52637 original size:35 final size:36
Alignment explanation
Indices: 52525--52807 Score: 258
Period size: 35 Copynumber: 7.7 Consensus size: 36
52515 ATTATATAGG
* *
52525 TTTTGAAAACATATATAATATACAGTTTTTAAAAAAAA
1 TTTTGAAAAC-TATATAATATATAGTTTTT-AAAAACA
*
52563 TTCTGAAAACTTATATAATATATAGTTTTTAAAACACA
1 TTTTGAAAAC-TATATAATATATAGTTTTTAAAA-ACA
52601 TTTTGAAAACTATATAATATAT-GATTTTT-AAAACA
1 TTTTGAAAACTATATAATATATAG-TTTTTAAAAACA
* * * *
52636 TTTTGAAAACTATAGAATATAGAGTTTTTGAAAGCA
1 TTTTGAAAACTATATAATATATAGTTTTTAAAAACA
* *
52672 TTTTGAAAATATATATAATATATAGTTTTTGAAAACA
1 TTTTGAAAA-CTATATAATATATAGTTTTTAAAAACA
* *
52709 -TTTAAAATAC-ATATAGTATATAG-TTTTAAAAACAA
1 TTTTGAAA-ACTATATAATATATAGTTTTTAAAAAC-A
* * *
52744 GTTTT-AAAAC-ATATATTATATGGTTTTGAAAATA-A
1 -TTTTGAAAACTATATAATATATAGTTTTTAAAA-ACA
*
52779 TTTTTAAAAAGCATATATAATATATAGTT
1 -TTTTGAAAA-C-TATATAATATATAGTT
52808 CTTTTTTTTT
Statistics
Matches: 208, Mismatches: 22, Indels: 29
0.80 0.08 0.11
Matches are distributed among these distances:
34 9 0.04
35 59 0.28
36 39 0.19
37 50 0.24
38 38 0.18
39 13 0.06
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.40
Consensus pattern (36 bp):
TTTTGAAAACTATATAATATATAGTTTTTAAAAACA
Found at i:52758 original size:72 final size:71
Alignment explanation
Indices: 52525--52775 Score: 214
Period size: 72 Copynumber: 3.5 Consensus size: 71
52515 ATTATATAGG
* * * * *
52525 TTTTGAAAACATATATAATATACAGTTTTTAAAAAAAATTCTGAAAACT-TATATAATATATAGT
1 TTTTGAAAACATATATAATATA-TGTTTTT-GAAAACATT-T-AAAA-TACATATAGTATATAGT
*
52589 TTTTAAAACACA
61 TTTAAAAACA-A
* *
52601 TTTTGAAAAC-TATATAATATATGATTTTT-AAAACATTTTGAAA-AC-TATAGAATATAGAGTT
1 TTTTGAAAACATATATAATATATG-TTTTTGAAAACA-TTTAAAATACATATAG--TATATAG-T
* *
52662 TTTGAAAGC-A
61 TTTAAAAACAA
*
52672 TTTTGAAAATATATATAATATATAGTTTTTGAAAACATTTAAAATACATATAGTATATAGTTTTA
1 TTTTGAAAACATATATAATATAT-GTTTTTGAAAACATTTAAAATACATATAGTATATAGTTTTA
52737 AAAACAA
65 AAAACAA
*
52744 GTTTT-AAAACATATAT--TATATGGTTTTGAAAA
1 -TTTTGAAAACATATATAATATATGTTTTTGAAAA
52776 TAATTTTTAA
Statistics
Matches: 147, Mismatches: 15, Indels: 33
0.75 0.08 0.17
Matches are distributed among these distances:
69 10 0.07
70 9 0.06
71 18 0.12
72 49 0.33
73 27 0.18
74 8 0.05
75 16 0.11
76 10 0.07
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.40
Consensus pattern (71 bp):
TTTTGAAAACATATATAATATATGTTTTTGAAAACATTTAAAATACATATAGTATATAGTTTTAA
AAACAA
Found at i:53154 original size:27 final size:27
Alignment explanation
Indices: 53116--53176 Score: 122
Period size: 27 Copynumber: 2.3 Consensus size: 27
53106 GCCCAAAAGC
53116 CACCGACGGCAGCGCGTGAGCATCATG
1 CACCGACGGCAGCGCGTGAGCATCATG
53143 CACCGACGGCAGCGCGTGAGCATCATG
1 CACCGACGGCAGCGCGTGAGCATCATG
53170 CACCGAC
1 CACCGAC
53177 AATATTACCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.23, C:0.36, G:0.31, T:0.10
Consensus pattern (27 bp):
CACCGACGGCAGCGCGTGAGCATCATG
Found at i:54149 original size:18 final size:19
Alignment explanation
Indices: 54126--54162 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
54116 TTATTTAATA
54126 TTCTTATTATTTT-TTATT
1 TTCTTATTATTTTCTTATT
54144 TTCTTATTATTTTCTTATT
1 TTCTTATTATTTTCTTATT
54163 ATTTTCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (19 bp):
TTCTTATTATTTTCTTATT
Found at i:54155 original size:11 final size:11
Alignment explanation
Indices: 54139--54170 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
54129 TTATTATTTT
54139 TTATTTTCTTA
1 TTATTTTCTTA
54150 TTATTTTCTTA
1 TTATTTTCTTA
54161 TTATTTTCTT
1 TTATTTTCTT
54171 TTTTTTTCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.75
Consensus pattern (11 bp):
TTATTTTCTTA
Found at i:55715 original size:98 final size:99
Alignment explanation
Indices: 55597--55789 Score: 316
Period size: 98 Copynumber: 2.0 Consensus size: 99
55587 TTATAATATT
* * *
55597 ATATATATATAATAAAGCTTGAGTTGTCTCTCTAAAGCAATTGGTTAAACGCCCCGGCTTTATGG
1 ATATATATATAATAAAGCTTGAGTTGTCCCACTAAAGCAATTGGTTAAACGCCCCGGATTTATGG
*
55662 ATAAGATTCAGCTATCCTGAT-AAGGTGATCGTA
66 ATAAGATTCAGCTAGCCTGATAAAGGTGATCGTA
* *
55695 ATATCTATATAATAAAGCTTGAGTTGTCCCACTAAAGCAATTGGTTAAATGCCCCGGATTTATGG
1 ATATATATATAATAAAGCTTGAGTTGTCCCACTAAAGCAATTGGTTAAACGCCCCGGATTTATGG
*
55760 ATAAGATTCATCTAGCCTGATAAAGGTGAT
66 ATAAGATTCAGCTAGCCTGATAAAGGTGAT
55790 TATAATATTG
Statistics
Matches: 87, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
98 79 0.91
99 8 0.09
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (99 bp):
ATATATATATAATAAAGCTTGAGTTGTCCCACTAAAGCAATTGGTTAAACGCCCCGGATTTATGG
ATAAGATTCAGCTAGCCTGATAAAGGTGATCGTA
Found at i:57421 original size:85 final size:85
Alignment explanation
Indices: 57260--57589 Score: 353
Period size: 85 Copynumber: 3.9 Consensus size: 85
57250 CTATTATAGT
* * * * * * *
57260 ATAGCTCAAGGCAATAAGGGTTATCTGTC-ACCAAAACCTTCAAGTTTGATTATATTCAGCTCAA
1 ATAGCTCAAGGCGAGAAGGGCTATATGTCAACCAAAACCTTCGAGTTCGATTACATTCAGCTCAA
* *
57324 GGACATATCAAATTTATAGT
66 GGACATATCAAATTTACAGC
* * *
57344 ATAACTCAAGGCGAGAAGGGTTATATGTCAACCAAATCCTTCGAGTTCGATTACATTCAGCTCAA
1 ATAGCTCAAGGCGAGAAGGGCTATATGTCAACCAAAACCTTCGAGTTCGATTACATTCAGCTCAA
* *
57409 GGGCATACCAAATTTACAGC
66 GGACATATCAAATTTACAGC
** * *
57429 ATAGCTCAAGGCGAGAAGGGCTATCGGTCAGA-AAAAACCTTCGAGTTCAATTACATTCAGCTCA
1 ATAGCTCAAGGCGAGAAGGGCTATATGTCA-ACCAAAACCTTCGAGTTCGATTACATTCAGCTCA
* *
57493 TA-AACATATCAAATTTACAAC
65 -AGGACATATCAAATTTACAGC
* ** * * * *
57514 ATAGCTCAAGGCGAGAAGGGCTATATGTCAA-TAAAAATTGTTGAGTTTGATTCCATTCAGCTCG
1 ATAGCTCAAGGCGAGAAGGGCTATATGTCAACCAAAACCT-TCGAGTTCGATTACATTCAGCTCA
*
57578 ATGACATATCAA
65 AGGACATATCAA
57590 TCACATGGTA
Statistics
Matches: 207, Mismatches: 34, Indels: 9
0.83 0.14 0.04
Matches are distributed among these distances:
84 32 0.15
85 173 0.84
86 2 0.01
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (85 bp):
ATAGCTCAAGGCGAGAAGGGCTATATGTCAACCAAAACCTTCGAGTTCGATTACATTCAGCTCAA
GGACATATCAAATTTACAGC
Found at i:57574 original size:170 final size:169
Alignment explanation
Indices: 57260--57576 Score: 395
Period size: 170 Copynumber: 1.9 Consensus size: 169
57250 CTATTATAGT
* * * ** ** *
57260 ATAGCTCAAGGCAATAAGGGTTATCTGTCACCAAAACCTTCAAGTTTGATTATATTCAGCTCAAG
1 ATAGCTCAAGGCAAGAAGGGCTATCGGTCAAAAAAACCTTCAAGTTCAATTACATTCAGCTCAAG
* * ** * **
57325 GACATATCAAATTTATAGTATAACTCAAGGCGAGAAGGGTTATATGTCAACCAAATCCTTCGAGT
66 AACATATCAAATTTACAACATAACTCAAGGCGAGAAGGGCTATATGTCAAAAAAATCCTTCGAGT
57390 TCGATTACATTCAGCTCAAGGGCATACCAAATTTACAGC
131 TCGATTACATTCAGCTCAAGGGCATACCAAATTTACAGC
* *
57429 ATAGCTCAAGGCGAGAAGGGCTATCGGTCAGAAAAAACCTTCGAGTTCAATTACATTCAGCTCAT
1 ATAGCTCAAGGCAAGAAGGGCTATCGGTCA-AAAAAACCTTCAAGTTCAATTACATTCAGCTCA-
* **
57494 A-AACATATCAAATTTACAACATAGCTCAAGGCGAGAAGGGCTATATGTCAATAAAAATTGTT-G
64 AGAACATATCAAATTTACAACATAACTCAAGGCGAGAAGGGCTATATGTCAA-AAAAATCCTTCG
* *
57557 AGTTTGATTCCATTCAGCTC
128 AGTTCGATTACATTCAGCTC
57577 GATGACATAT
Statistics
Matches: 123, Mismatches: 22, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
169 26 0.21
170 90 0.73
171 7 0.06
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (169 bp):
ATAGCTCAAGGCAAGAAGGGCTATCGGTCAAAAAAACCTTCAAGTTCAATTACATTCAGCTCAAG
AACATATCAAATTTACAACATAACTCAAGGCGAGAAGGGCTATATGTCAAAAAAATCCTTCGAGT
TCGATTACATTCAGCTCAAGGGCATACCAAATTTACAGC
Found at i:59081 original size:22 final size:23
Alignment explanation
Indices: 59053--59100 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
59043 ACCTTGGACA
*
59053 AAAAT-AATATAAT-AAAATTAAT
1 AAAATAAATA-AATAAAAATAAAT
59075 AAAATAAATAAATAAAAATAAAT
1 AAAATAAATAAATAAAAATAAAT
59098 AAA
1 AAA
59101 CAAATAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (23 bp):
AAAATAAATAAATAAAAATAAAT
Found at i:59097 original size:18 final size:18
Alignment explanation
Indices: 59076--59112 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
59066 AAAATTAATA
*
59076 AAATAAATAAATAAAAAT
1 AAATAAACAAATAAAAAT
*
59094 AAATAAACAAATAATAAT
1 AAATAAACAAATAAAAAT
59112 A
1 A
59113 TTTTTTCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.22
Consensus pattern (18 bp):
AAATAAACAAATAAAAAT
Found at i:59112 original size:14 final size:14
Alignment explanation
Indices: 59075--59110 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
59065 TAAAATTAAT
*
59075 AAAATAAATAAATA
1 AAAATAAATAAACA
59089 AAAATAAATAAACA
1 AAAATAAATAAACA
59103 AATAATAA
1 AA-AATAA
59111 TATTTTTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (14 bp):
AAAATAAATAAACA
Found at i:59149 original size:2 final size:2
Alignment explanation
Indices: 59138--59168 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
59128 TTTAAAATTG
59138 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
59169 AAAAAGTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:59190 original size:24 final size:24
Alignment explanation
Indices: 59161--59207 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
59151 TATATATATA
59161 TATATATAAAAAAGTTTTCAAAAC
1 TATATATAAAAAAGTTTTCAAAAC
* * *
59185 TATATATTATATAGTTTTCAAAA
1 TATATATAAAAAAGTTTTCAAAA
59208 TGTTTTCAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.40
Consensus pattern (24 bp):
TATATATAAAAAAGTTTTCAAAAC
Found at i:59213 original size:35 final size:35
Alignment explanation
Indices: 59169--59375 Score: 200
Period size: 35 Copynumber: 6.1 Consensus size: 35
59159 TATATATATA
*
59169 AAAAAGTTTTCAAAACTATATATTATATAGTTTTC
1 AAAATGTTTTCAAAACTATATATTATATAGTTTTC
* *
59204 AAAATGTTTTCAAAATTATATATTATATATTTTTC
1 AAAATGTTTTCAAAACTATATATTATATAGTTTTC
* * *
59239 AAAATATTTTTTAAAAACCATATATTATATATGTTTTC
1 -AAA-ATGTTTTCAAAACTATATATTATATA-GTTTTC
*
59277 AAAACGTTTTCAAAAC-------TATATA-TTTTC
1 AAAATGTTTTCAAAACTATATATTATATAGTTTTC
* * *
59304 AAAATGTTTTAAAAACTATATAATATATA-TTTTT
1 AAAATGTTTTCAAAACTATATATTATATAGTTTTC
*
59338 GAAATGTTTTCAAAAACTATATA-TATATATGTTTTC
1 AAAATGTTTTC-AAAACTATATATTATATA-GTTTTC
59374 AA
1 AA
59376 TACTATATAT
Statistics
Matches: 141, Mismatches: 18, Indels: 25
0.77 0.10 0.14
Matches are distributed among these distances:
27 19 0.13
29 6 0.04
34 25 0.18
35 43 0.30
36 18 0.13
37 25 0.18
38 5 0.04
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (35 bp):
AAAATGTTTTCAAAACTATATATTATATAGTTTTC
Found at i:59296 original size:27 final size:27
Alignment explanation
Indices: 59266--59325 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
59256 CCATATATTA
* *
59266 TATATGTTTTCAAAACGTTTTCAAAAC
1 TATATATTTTCAAAACGTTTTAAAAAC
*
59293 TATATATTTTCAAAATGTTTTAAAAAC
1 TATATATTTTCAAAACGTTTTAAAAAC
59320 TATATA
1 TATATA
59326 ATATATATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.43
Consensus pattern (27 bp):
TATATATTTTCAAAACGTTTTAAAAAC
Found at i:59336 original size:34 final size:36
Alignment explanation
Indices: 59293--59375 Score: 125
Period size: 34 Copynumber: 2.4 Consensus size: 36
59283 TTTTCAAAAC
59293 TATATATTTTCAAAATGTTTT-AAAAACTATATA-A
1 TATATATTTTCAAAATGTTTTCAAAAACTATATATA
**
59327 TATATATTTTTGAAATGTTTTCAAAAACTATATATA
1 TATATATTTTCAAAATGTTTTCAAAAACTATATATA
*
59363 TATATGTTTTCAA
1 TATATATTTTCAA
59376 TACTATATAT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
34 19 0.45
35 12 0.29
36 11 0.26
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.47
Consensus pattern (36 bp):
TATATATTTTCAAAATGTTTTCAAAAACTATATATA
Found at i:59385 original size:24 final size:24
Alignment explanation
Indices: 59341--59390 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
59331 TATTTTTGAA
59341 ATGTTTTCAAAAACTATATATATAT
1 ATGTTTTCAAAAACTATATAT-TAT
*
59366 ATGTTTTC-AATACTATATATTAT
1 ATGTTTTCAAAAACTATATATTAT
59389 AT
1 AT
59391 TTTCGAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 5 0.21
24 11 0.46
25 8 0.33
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.48
Consensus pattern (24 bp):
ATGTTTTCAAAAACTATATATTAT
Found at i:59424 original size:59 final size:59
Alignment explanation
Indices: 59242--59424 Score: 140
Period size: 61 Copynumber: 3.0 Consensus size: 59
59232 ATTTTTCAAA
* * * * * * *
59242 ATATTTTTTAAAAACCATATATTATATATGTTTTCAAAACGTTTTC-AAAACTATATATTTT
1 ATATGTTTTAAAAA-C-TATATAATATATATTTTCGAAATGTTTTCAAAAAATATATA-TAT
* * *
59303 CAAAATGTTTTAAAAACTATATAATATATATTTTTGAAATGTTTTCAAAAACTATATATAT
1 --ATATGTTTTAAAAACTATATAATATATATTTTCGAAATGTTTTCAAAAAATATATATAT
* * * *
59364 ATATGTTTTCAATACTATAT-AT-TATATTTTCGAAAATCGATTTTTAAAAAATTTAT-TAT
1 ATATGTTTTAAAAACTATATAATATATATTTTCG-AAAT-G-TTTTCAAAAAATATATATAT
59423 AT
1 AT
59425 CTTCAAAAAA
Statistics
Matches: 101, Mismatches: 15, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
57 9 0.09
58 6 0.06
59 23 0.23
60 13 0.13
61 26 0.26
62 12 0.12
63 12 0.12
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (59 bp):
ATATGTTTTAAAAACTATATAATATATATTTTCGAAATGTTTTCAAAAAATATATATAT
Found at i:60323 original size:84 final size:85
Alignment explanation
Indices: 60055--60387 Score: 388
Period size: 84 Copynumber: 3.9 Consensus size: 85
60045 TACCATGCAG
* * * * * *
60055 TTGATATGTCATCGAGTTGAATGGAATCAAACTCGACA-GTTTTTGTTGACAGATAGCCCTTCTC
1 TTGATATGTCCTTGAGCTGAATGTAATCAAACTCGA-AGGTTTTGGTTGACAGATAACCCTTCTC
* *
60119 TCCTTGAGCTATGC-AGTAAAT
65 GCCTTGAGCTATACTA-TAAAT
* *
60140 TTGATATG-CCTTTGAGCTGAATGTAATCAAACTCGAAGGTTTTTTGCTGACAGATAACCCTTCT
1 TTGATATGTCC-TTGAGCTGAATGTAATCAAACTCGAAGG-TTTTGGTTGACAGATAACCCTTCT
* *
60204 CGCCTTGAGCTATGCTGTAAAT
64 CGCCTTGAGCTATACTATAAAT
* * * * *
60226 TTGGTATGCCCTTGAGCTGAATGTAATCGAACTCGAAGG-TTTGGTTGACAGATAACCCTTTTTG
1 TTGATATGTCCTTGAGCTGAATGTAATCAAACTCGAAGGTTTTGGTTGACAGATAACCCTTCTCG
*
60290 CCTTGAGTTATACTATAAAT
66 CCTTGAGCTATACTATAAAT
* * * *
60310 TTAATATGTCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTGG-TGACAAATAACCCTTCTCA
1 TTGATATGTCCTTGAGCTGAATGTAATCAAACTCGAAGGTTTTGGTTGACAGATAACCCTTCTCG
*
60374 CCTTGAGTTATACT
66 CCTTGAGCTATACT
60388 GTAATAGGCT
Statistics
Matches: 218, Mismatches: 24, Indels: 13
0.85 0.09 0.05
Matches are distributed among these distances:
84 105 0.48
85 36 0.17
86 75 0.34
87 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.35
Consensus pattern (85 bp):
TTGATATGTCCTTGAGCTGAATGTAATCAAACTCGAAGGTTTTGGTTGACAGATAACCCTTCTCG
CCTTGAGCTATACTATAAAT
Found at i:65853 original size:15 final size:15
Alignment explanation
Indices: 65833--65877 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 15
65823 AGAAAAAAGT
65833 AATAATAAAATAAAA
1 AATAATAAAATAAAA
65848 AATAATAAGAAAATAAAA
1 AATAAT---AAAATAAAA
*
65866 AATAACAAAATA
1 AATAATAAAATA
65878 GAAATAATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 12 0.46
18 14 0.54
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.18
Consensus pattern (15 bp):
AATAATAAAATAAAA
Found at i:65853 original size:18 final size:18
Alignment explanation
Indices: 65825--65870 Score: 74
Period size: 18 Copynumber: 2.5 Consensus size: 18
65815 AGAAAAAGAG
*
65825 AAAAAAGTAATAATAAAAT
1 AAAAAA-TAATAAGAAAAT
65844 AAAAAATAATAAGAAAAT
1 AAAAAATAATAAGAAAAT
65862 AAAAAATAA
1 AAAAAATAA
65871 CAAAATAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 20 0.77
19 6 0.23
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.17
Consensus pattern (18 bp):
AAAAAATAATAAGAAAAT
Done.